[gmx-users] genion halted

[Sampo Karkola]

Hi,

so you got genion working with 4.0.2?

Sampo

andrea spitaleri wrote:
> gcc-4.0.2 seems ok for gmx-3.3.1
> I have also submitted in bugzilla a similar problem with g_rdf
> 
> 
> Regards
> 
> andrea
> 
> Sampo Karkola wrote:
>> Hi,
>>
>> the same one, gcc-4.1. Have you tried with other versions?
>>
>> Sampo
>>
>> andrea spitaleri wrote:
>>> Hi
>>> which gcc have you used for compiling gromacs? I have the same problem
>>> in one pc in which I have
>>> build gromacs using gcc-4.1
>>>
>>> Regards
>>>
>>> andrea
>>>
>>> Sampo Karkola wrote:
>>>> Dear list,
>>>>
>>>> the genion program gets halted when I'm trying to replace the solvent
>>>> molecules with ions. The command
>>>>
>>>> genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top
>>>> -pname NA+ -nname CL- -random -neutral -conc 0.1
>>>>
>>>> asks for the group of solvent molecules and when I tell him to use it I
>>>> get this output
>>>>
>>>> Selected 12: 'SOL'
>>>> Number of (3-atomic) solvent molecules: 9918
>>>>
>>>> Processing topology
>>>> Replacing 9875 solute molecules in topology file (fdt.top)  by 22 NA+
>>>> and 21 CL- ions.
>>>>
>>>> Back Off! I just backed up fdt.top to ./#fdt.top.2#
>>>> Replacing solvent molecule 1163 (atom 6250) with NA+
>>>>
>>>> and then nothing happens. genion.log gets generated only half way. My
>>>> system is Ubuntu 6.10 on AMD AthlonX2 and I've tried the packages via
>>>> synaptic and also built from source. The same thing happens in both of
>>>> them. Gromacs version is 3.3.1. However, when I try the same thing on
>>>> another machine, a HP Proliant ML350 with Debian Sarge and Gromacs
>>>> 3.3.1, everything goes well.
>>>>
>>>> None of the gromacs programs gives any errors before genion.
>>>>
>>>> I'll give you more info about the system configuration if anyone asks :)
>>>>
>>>> Sampo
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>